Am trying to read in a vcf file to R. The vcf is from the 1000 G project here -

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/functional_annotation/filtered/

so the code

library(VariantAnnotation)
ScanVcfParam(info=c("EAS_AF","EUR_AF","AFR_AF","AMR_AF","SAS_AF","CSQ"))->param
readVcf("ALL.chr2.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.annotation.vcf.gz","hg19",param=param)->cff
length((info(cff)[["CSQ"]]))

The original vcf file has a column with the position (POS) col 2 - however, that is not accessible in the file afterwards.

Also

info(header(cff)):

               Number Type    Description                                  
   CIEND           2      Integer Confidence interval around END for impreci...
   CIPOS           2      Integer Confidence interval around POS for impreci...
   CS              1      String  Source call set.                             
   END             1      Integer End coordinate of this variant               
   IMPRECISE       0      Flag    Imprecise structural variation               
   MC              .      String  Merged calls.                                
   MEINFO          4      String  Mobile element info of the form NAME,START...
   MEND            1      Integer Mitochondrial end coordinate of inserted s...
   MLEN            1      Integer Estimated length of mitochondrial insert     
   MSTART          1      Integer Mitochondrial start coordinate of inserted...
   SVLEN           .      Integer Difference in length between REF and ALT a...
   SVTYPE          1      String  Type of structural variant                   
   TSD             1      String  Precise Target Site Duplication for bases,...
   AC              A      Integer Total number of alternate alleles in calle...
   AF              A      Float   Estimated allele frequency in the range (0,1)
   NS              1      Integer Number of samples with data                  
   AN              1      Integer Total number of alleles in called genotypes  
   EAS_AF          A      Float   Allele frequency in the EAS populations ca...#
   EUR_AF          A      Float   Allele frequency in the EUR populations ca...#
   AFR_AF          A      Float   Allele frequency in the AFR populations ca...#
   AMR_AF          A      Float   Allele frequency in the AMR populations ca...#
   SAS_AF          A      Float   Allele frequency in the SAS populations ca...#
   DP              1      Integer Total read depth                             
   AA              1      String  Ancestral Allele. Format: AA|REF|ALT|Indel...
   CSQ             .      String  Consequence type as predicted by VEP WITH ...#
   GENCODE         .      String  The annotation of coding variants and spli...#
   ALOFT           A      String  The Annotation Of Loss-of-Function Transcr...#
   PHOSPHORYLATION A      String  Predicted as phosphorylation sites by Phos...
   ERB             .      String  Ensembl Regulatory Build. Format: Allele|G...
   HighD           .      String  The Super population with the higher deriv...#
   FUNSEQ          A      Float   FunSeq score for noncoding SNV             

prints a list of parameters to do a selection on. However, the POS column is not among them. How can I get the positions of all the variants in the vcf?

The VCF object is a "RangedSummarizedExperiment", so it implements range accessors for getting position information. The start() accessor should give you the position. Also, the underlying GRanges is accessible with rowRanges().